The deposition pattern of plant cell walls influences the nature of plant body, such as size, shape, and stiffness. In xylem vessels, cell wall deposition is locally inhibited to form pits, which are tiny caves in cell walls that allow waters move through xylem vessels. Our research group revealed the regulatory mechanism of the pit formation by combining the genetic approach and mathematical approach known as “reaction-diffusion system”. The knowledge obtained in our research may contribute to developing new plants of modified size and stiffness by artificially regulating the deposition pattern of cell walls.